`scanpy.external.pp.harmony_integrate` incompatible with newly updated `harmonypy>=0.1.0`

[kiklata]

What kind of feature would you like to request?

Additional function parameters / changed functionality / changed defaults?

Please describe your wishes

scanpy.external.pp.harmony_integrate assumes the old harmonypy output format and applies Z_corr.T.
However, since harmonypy>=0.1.0, Z_corr is already returned in cells × PCs format, so the transpose is no longer needed. This leads to shape mismatches or incorrect embeddings.

[dylkot]

I have run into this issue as well. It should be:

adata.obsm[adjusted_basis] = harmony_out.Z_corr

rather than

adata.obsm[adjusted_basis] = harmony_out.Z_corr.T

at scanpy/external/pp/_harmony_integrate.py:99

[flying-sheep]

We’re going to get rid of sc.external (#2717), but having a torch-less harmony implementation in scanpy isn’t out of the question!

cc @Intron7